ID code: '4GAT' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 1042 C1' C B 101 beta 1038 1043 1041 1073 C1' A B 102 beta 1069 1074 1072 1105 C1' G B 103 beta 1101 1106 1104 1138 C1' C B 104 beta 1134 1139 1137 1168 C1' G B 105 beta 1164 1169 1167 1201 C1' A B 106 beta 1197 1202 1200 1233 C1' T B 107 beta 1229 1234 1232 1265 C1' A B 108 beta 1261 1266 1264 1297 C1' G B 109 beta 1293 1298 1296 1330 C1' A B 110 beta 1326 1331 1329 1362 C1' G B 111 beta 1358 1363 1361 1395 C1' A B 112 beta 1391 1396 1394 1427 C1' C B 113 beta 1423 1428 1426 1456 C1' G C 114 beta 1452 1457 1455 1490 C1' T C 115 beta 1486 1491 1489 1522 C1' C C 116 beta 1518 1523 1521 1552 C1' T C 117 beta 1548 1553 1551 1584 C1' C C 118 beta 1580 1585 1583 1614 C1' T C 119 beta 1610 1615 1613 1646 C1' A C 120 beta 1642 1647 1645 1678 C1' T C 121 beta 1674 1679 1677 1710 C1' C C 122 beta 1706 1711 1709 1740 C1' G C 123 beta 1736 1741 1739 1773 C1' C C 124 beta 1769 1774 1772 1803 C1' T C 125 beta 1799 1804 1802 1835 C1' G C 126 beta 1831 1836 1834 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 1041 C2' C B 101 1042 1039 1072 C2' A B 102 1073 1070 1104 C2' G B 103 1105 1102 1137 C2' C B 104 1138 1135 1167 C2' G B 105 1168 1165 1200 C2' A B 106 1201 1198 1232 C2' T B 107 1233 1230 1264 C2' A B 108 1265 1262 1296 C2' G B 109 1297 1294 1329 C2' A B 110 1330 1327 1361 C2' G B 111 1362 1359 1394 C2' A B 112 1395 1392 1426 C2' C B 113 1427 1424 1455 C2' G C 114 1456 1453 1489 C2' T C 115 1490 1487 1521 C2' C C 116 1522 1519 1551 C2' T C 117 1552 1549 1583 C2' C C 118 1584 1581 1613 C2' T C 119 1614 1611 1645 C2' A C 120 1646 1643 1677 C2' T C 121 1678 1675 1709 C2' C C 122 1710 1707 1739 C2' G C 123 1740 1737 1772 C2' C C 124 1773 1770 1802 C2' T C 125 1803 1800 1834 C2' G C 126 1835 1832 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 1039 C3' C B 101 OK 1037 1040 1041 1070 C3' A B 102 OK 1068 1071 1072 1102 C3' G B 103 OK 1100 1103 1104 1135 C3' C B 104 OK 1133 1136 1137 1165 C3' G B 105 OK 1163 1166 1167 1198 C3' A B 106 OK 1196 1199 1200 1230 C3' T B 107 OK 1228 1231 1232 1262 C3' A B 108 OK 1260 1263 1264 1294 C3' G B 109 OK 1292 1295 1296 1327 C3' A B 110 OK 1325 1328 1329 1359 C3' G B 111 OK 1357 1360 1361 1392 C3' A B 112 OK 1390 1393 1394 1424 C3' C B 113 OK 1422 1425 1426 1453 C3' G C 114 OK 1451 1454 1455 1487 C3' T C 115 OK 1485 1488 1489 1519 C3' C C 116 OK 1517 1520 1521 1549 C3' T C 117 OK 1547 1550 1551 1581 C3' C C 118 OK 1579 1582 1583 1611 C3' T C 119 OK 1609 1612 1613 1643 C3' A C 120 OK 1641 1644 1645 1675 C3' T C 121 OK 1673 1676 1677 1707 C3' C C 122 OK 1705 1708 1709 1737 C3' G C 123 OK 1735 1738 1739 1770 C3' C C 124 OK 1768 1771 1772 1800 C3' T C 125 OK 1798 1801 1802 1832 C3' G C 126 OK 1830 1833 1834 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1037 C4' C B 101 OK 1039 1036 1038 1068 C4' A B 102 OK 1070 1067 1069 1100 C4' G B 103 OK 1102 1099 1101 1133 C4' C B 104 OK 1135 1132 1134 1163 C4' G B 105 OK 1165 1162 1164 1196 C4' A B 106 OK 1198 1195 1197 1228 C4' T B 107 OK 1230 1227 1229 1260 C4' A B 108 OK 1262 1259 1261 1292 C4' G B 109 OK 1294 1291 1293 1325 C4' A B 110 OK 1327 1324 1326 1357 C4' G B 111 OK 1359 1356 1358 1390 C4' A B 112 OK 1392 1389 1391 1422 C4' C B 113 OK 1424 1421 1423 1451 C4' G C 114 OK 1453 1450 1452 1485 C4' T C 115 OK 1487 1484 1486 1517 C4' C C 116 OK 1519 1516 1518 1547 C4' T C 117 OK 1549 1546 1548 1579 C4' C C 118 OK 1581 1578 1580 1609 C4' T C 119 OK 1611 1608 1610 1641 C4' A C 120 OK 1643 1640 1642 1673 C4' T C 121 OK 1675 1672 1674 1705 C4' C C 122 OK 1707 1704 1706 1735 C4' G C 123 OK 1737 1734 1736 1768 C4' C C 124 OK 1770 1767 1769 1798 C4' T C 125 OK 1800 1797 1799 1830 C4' G C 126 OK 1832 1829 1831 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 1036 C5' C B 101 1035 1037 1067 C5' A B 102 1066 1068 1099 C5' G B 103 1098 1100 1132 C5' C B 104 1131 1133 1162 C5' G B 105 1161 1163 1195 C5' A B 106 1194 1196 1227 C5' T B 107 1226 1228 1259 C5' A B 108 1258 1260 1291 C5' G B 109 1290 1292 1324 C5' A B 110 1323 1325 1356 C5' G B 111 1355 1357 1389 C5' A B 112 1388 1390 1421 C5' C B 113 1420 1422 1450 C5' G C 114 1449 1451 1484 C5' T C 115 1483 1485 1516 C5' C C 116 1515 1517 1546 C5' T C 117 1545 1547 1578 C5' C C 118 1577 1579 1608 C5' T C 119 1607 1609 1640 C5' A C 120 1639 1641 1672 C5' T C 121 1671 1673 1704 C5' C C 122 1703 1705 1734 C5' G C 123 1733 1735 1767 C5' C C 124 1766 1768 1797 C5' T C 125 1796 1798 1829 C5' G C 126 1828 1830 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1063 P A B 102 OK OK 1040 1064 1065 1066 1095 P G B 103 OK OK 1071 1096 1097 1098 1128 P C B 104 OK OK 1103 1129 1130 1131 1158 P G B 105 OK OK 1136 1159 1160 1161 1191 P A B 106 OK OK 1166 1192 1193 1194 1223 P T B 107 OK OK 1199 1224 1225 1226 1255 P A B 108 OK OK 1231 1256 1257 1258 1287 P G B 109 OK OK 1263 1288 1289 1290 1320 P A B 110 OK OK 1295 1321 1322 1323 1352 P G B 111 OK OK 1328 1353 1354 1355 1385 P A B 112 OK OK 1360 1386 1387 1388 1417 P C B 113 OK OK 1393 1418 1419 1420 1480 P T C 115 OK OK 1454 1481 1482 1483 1512 P C C 116 OK OK 1488 1513 1514 1515 1542 P T C 117 OK OK 1520 1543 1544 1545 1574 P C C 118 OK OK 1550 1575 1576 1577 1604 P T C 119 OK OK 1582 1605 1606 1607 1636 P A C 120 OK OK 1612 1637 1638 1639 1668 P T C 121 OK OK 1644 1669 1670 1671 1700 P C C 122 OK OK 1676 1701 1702 1703 1730 P G C 123 OK OK 1708 1731 1732 1733 1763 P C C 124 OK OK 1738 1764 1765 1766 1793 P T C 125 OK OK 1771 1794 1795 1796 1825 P G C 126 OK OK 1801 1826 1827 1828 ---------------------------------------------------------------------------------